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Nat Commun 2016 Feb 25;7:8674. doi: 10.1038/ncomms9674.
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A workflow to process 3D+time microscopy images of developing organisms and reconstruct their cell lineage.

Faure E , Savy T , Rizzi B , Melani C , Stašová O , Fabrèges D , Špir R , Hammons M , Čúnderlík R , Recher G , Lombardot B , Duloquin L , Colin I , Kollár J , Desnoulez S , Affaticati P , Maury B , Boyreau A , Nief JY , Calvat P , Vernier P , Frain M , Lutfalla G , Kergosien Y , Suret P , Remešíková M , Doursat R , Sarti A , Mikula K , Peyriéras N , Bourgine P .

The quantitative and systematic analysis of embryonic cell dynamics from in vivo 3D+time image data sets is a major challenge at the forefront of developmental biology. Despite recent breakthroughs in the microscopy imaging of living systems, producing an accurate cell lineage tree for any developing organism remains a difficult task. We present here the BioEmergences workflow integrating all reconstruction steps from image acquisition and processing to the interactive visualization of reconstructed data. Original mathematical methods and algorithms underlie image filtering, nucleus centre detection, nucleus and membrane segmentation, and cell tracking. They are demonstrated on zebrafish, ascidian and sea urchin embryos with stained nuclei and membranes. Subsequent validation and annotations are carried out using Mov-IT, a custom-made graphical interface. Compared with eight other software tools, our workflow achieved the best lineage score. Delivered in standalone or web service mode, BioEmergences and Mov-IT offer a unique set of tools for in silico experimental embryology.

PubMed ID: 26912388
PMC ID: PMC4773431
Article link: Nat Commun

Species referenced: Echinodermata
Genes referenced: dr1 LOC100887844 LOC100893907 LOC115919910 LOC115925415 LOC583082 pole

Article Images: [+] show captions
References [+] :
Amat, Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. 2014, Pubmed